A systematic review and a comprehensive approach to PhD students' wellbeing

The pursuit of a doctoral degree is a challenging process that can have a negative impact on the wellbeing of PhD students. Therefore, the aim here is to offer a systematic review of the current state of the literature on wellbeing among PhD students and the variables it involves in order to build an integrative model that will enrich future research. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology for systematic reviews has been used to lay out the process in a flow diagram. We systematically review studies up to 2021 (N = 38) published on the Web of Science and SCOPUS databases. The results show the current state of the literature on wellbeing in PhD students, the characteristics of the studies (location, study design, and sample), how the literature defines the concept, the variables involved, the study limitations, and future perspectives to improve the quality of life of doctoral students. Finally, a comprehensive approach to the topic is presented in an integrative model that encompasses all variables identified in the literature and offers a guide for future research.

Pharmacogenetic biomarkers for secukinumab response in psoriasis patients in real-life clinical practice

BACKGROUND

Prediction of the response to a biological treatment in psoriasis patients would allow efficient treatment allocation.

OBJECTIVE

To identify polymorphisms associated with secukinumab response in psoriasis patients in a daily practice setting.

METHODS

We studied 180 SNPs in patients with moderate-to-severe plaque psoriasis recruited from 15 Spanish hospitals. Treatment effectiveness was evaluated by absolute PASI ≤3 and ≤1 at 6 and 12 months. Individuals were genotyped using a custom Taqman array. Multiple logistic regression models were generated. Sensitivity, specificity and area under the curve (AUC) were analysed.

RESULTS

A total of 173 patients were studied at 6 months, (67% achieved absolute PASI ≤ 3 and 65% PASI ≤ 1) and 162 at 12 months (75% achieved absolute PASI ≤ 3 and 64% PASI ≤ 1). Multivariable analysis showed the association of different sets of SNPs with the response to secukinumab. The model of absolute PASI≤3 at 6 months showed best values of sensitivity and specificity. Four SNPs were associated with the capability of achieving absolute PASI ≤ 3 at 6 months. rs1801274 (FCGR2A), rs2431697 (miR-146a) and rs10484554 (HLCw6) were identified as risk factors for failure to achieve absolute PASI≤3, while rs1051738 (PDE4A) was protective. AUC including these genotypes, weight of patients and history of biological therapy was 0.88 (95% CI 0.83-0.94), with a sensitivity of 48.6% and specificity of 95.7% to discriminate between both phenotypes.

CONCLUSION

We have identified a series of polymorphisms associated with the response to secukinumab capable of predicting the potential response/non-response to this drug in patients with plaque psoriasis.

Analysis of penitentiary, social and legal operators’ perceptions of prison inmates with intellectual disabilities

Objective

To analyze the different perceptions of professionals about the problem of intellectual disability in the prison setting.

Material and method

Exploratory-descriptive type. In-depth interviews with legal, social and prison operators of Centro Penitenciario de Zuera (Zaragoza).

Results

The narratives of the interviewed subjects point to the aggravating circumstances that a closed social environment can entail for inmates with intellectual disabilities. Communications in the prison administration are written in a technical language that is not understandable for inmates with intellectual deficits.

Discusion

There is a need to give more visibility to the case of inmates with intellectual disabilities. Procedures also need to be applied that favour greater cognitive accessibility for this profile of inmates, along with the promotion of awareness raising and training for professionals to enable them to deal with this issue.

Significance of a polymerase chain reaction method in the detection of Clostridioides difficile

OBJECTIVE

Clostridioides difficile (CD) is the most common cause of nosocomial diarrhea. Detection of CD toxin in patients' faecal samples is the traditional rapid method for the diagnosis of CD infection. Various testing algorithms have been proposed: an initial screening test using a rapid test, and a confirmatory test (cytotoxicity neutralization assay, toxigenic culture, nucleic acid amplification test) for discordant results. The aim of this study was to evaluate the effectiveness of a two-step algorithm using an immunochromatographic test followed of a polymerase chain reaction (PCR).

METHODS

The specimens have been tested according to the following schedule: 1) Step one: All samples were tested for detection of glutamate dehydrogenase antigen (GDH) and toxin A/B using the C. diff QUIK CHEK Complete test. All GDH and toxins positive results were considered CD positives; 2) Step two: When the results were discrepant (only GDH+ or toxins+), the samples were confirmed using the PCR test BD MAX Cdiff. All PCR positive results were considered CD positives.

RESULTS

A total of 2,138 specimens were initially tested. 139 were positive for GDH and toxins. 160 discrepant results (148 GDH+ and 12 toxins+) were tested by PCR, 117 were positive (107/148 GDH+ and 10/12 toxins+).

CONCLUSIONS

The implementation of a PCR method showed an increase de 117 positive results (73.1% of discrepant). Considering the sensitivity of C.diff QUIK CHEK (instructions of manufacturer), the GDH discrepant results may be false negatives, y the samples PCR and toxins positives may be real positives results.

Impact of SARS-CoV-2 pandemic among health care workers in a secondary teaching hospital in Spain

BACKGROUND

The COVID-19 pandemic has posed a huge challenge to healthcare systems and their personnel worldwide. The study of the impact of SARS-CoV-2 infection among healthcare workers (HCW), through prevalence studies, will let us know viral expansion, individuals at most risk and the most exposed areas in healthcare organizations. The aim of this study is to gauge the impact of SARS-CoV-2 pandemic in our hospital workforce and identify groups and areas at increased risk.

METHODS AND FINDINGS

This is a cross-sectional and incidence study carried out on healthcare workers based on molecular and serological diagnosis of SARS-CoV-2 infection. Of the 3013 HCW invited to participate, 2439 (80.9%) were recruited, including 674 (22.4%) who had previously consulted at the Occupational Health Service (OHS) for confirmed exposure and/or presenting symptoms suggestive of COVID-19. A total of 411 (16.9%) and 264 (10.8%) healthcare workers were SARS-CoV-2 IgG and rRT-PCR positive, respectively. The cumulative prevalence considering all studies (IgG positive HCW and/or rRT-PCR positive detection) was 485 (19.9%). SARS-CoV-2 IgG-positive patients in whom the virus was not detected were 221 (9.1%); up to 151 of them (68.3%) did not report any compatible symptoms nor consult at the OHS for this reason. Men became more infected than women (25% vs 18.5%, p = 0.0009), including when data were also classified by age. COVID-19 cumulative prevalence among the HCW assigned to medical departments was higher (25.2%) than others, as well as among medical staff (25.4%) compared with other professional categories (p<0.01).

CONCLUSIONS

The global impact of the COVID-19 pandemic on HCW of our centre has been 19.9%. Doctors and medical services personnel have had the highest prevalence of SARS-CoV-2 infection, but many of them have not presented compatible symptoms. This emphasizes the performance of continuous surveillance methods of the most exposed health personnel and not only based on the appearance of symptoms.

Role of asymptomatic and symptomatic humans as reservoirs of visceral leishmaniasis in a Mediterranean context

Background

In the Mediterranean basin, Leishmania infantum is the causative agent of visceral leishmaniasis (VL), a zoonosis in which the dog is the primary domestic reservoir, although wildlife may have a leading role in the sylvatic cycle of the disease in some areas. Infections without disease are very frequent. There is limited information regarding the role that VL patients and asymptomatic infected individuals could be playing in the transmission of L. infantum. Xenodiagnosis of leishmaniasis has been used in this descriptive study to explore the role of symptomatic and asymptomatic infected individuals as reservoirs in a recent focus of leishmaniasis in southwestern Madrid, Spain.

Methodology and main findings

Asymptomatic blood donors (n = 24), immunocompetent patients who were untreated (n = 12) or treated (n = 11) for visceral leishmaniasis (VL), and immunocompromised patients with VL (n = 3) were enrolled in the study. Their infectivity to Phlebotomus perniciosus was studied by indirect xenodiagnosis on peripheral blood samples. Quantitative polymerase chain reaction of blood samples from immunocompetent patients untreated for VL and immunocompromised untreated, treated and under secondary prophylaxis for VL was performed. Antibodies against Leishmania were studied by indirect fluorescent antibody and rK39-immunochromatographic tests. A lymphoproliferative assay with a soluble Leishmania antigen was used to screen for leishmaniasis infection in the healthy population. Sixty-two xenodiagnostic tests were carried out and 5,080 sand flies were dissected. Positive xenodiagnosis was recorded in four patients, with different sand fly infection rates: 1 immunosuppressed HIV / L. infantum coinfected asymptomatic patient, 1 immunosuppressed patient with multiple myeloma and symptomatic active VL, and 2 immunocompetent patients with untreated active VL. All blood donors were negative for both xenodiagnosis and conventional PCR.

Conclusions / Significance

There is no consensus amongst authors on the definition of an ‘asymptomatic case’ nor on the tools for screening; we, therefore, have adopted one for the sake of clarity. Immunocompetent subjects, both infected asymptomatics and those treated for VL, are limited in number and appear to have no epidemiological relevance. The impact is limited for immunocompetent patients with untreated active VL, whilst immunosuppressed individuals undergoing immunosuppressive therapy and immunosuppressed individuals HIV / L. infantum coinfected were the most infectious towards sand flies. It is noteworthy that the HIV / L. infantum coinfected patient with asymptomatic leishmaniasis was easily infectious to sand flies for a long time, despite being under continuous prophylaxis for leishmaniasis. Accordingly, screening for latent Leishmania infection in HIV-infected patients is recommended in scenarios where transmission occurs. In addition, screening for VL in HIV-infected patients who have spent time in VL-endemic areas should also be implemented in non-endemic areas. More research is needed to better understand if some asymptomatic coinfected individuals contribute to transmission as ‘super-spreaders’.

Leishmaniasis is a set of diseases caused by Leishmania parasites and transmitted through the bites of infected phlebotomine sand fly females during blood ingestion. Visceral leishmaniasis (VL) is caused by Leishmania infantum in the Mediterranean region and dog is the primary domestic reservoir, although we can not ignore the role that wild reservoirs can have under certain conditions. As for the role of the human host in the transmission of the disease is not fully understood. The present work explores this important epidemiological aspect to try to clarify it. The study concludes that asymptomatic infected individuals and the immunocompetent patients treated for VL have no epidemiological impact in the transmission of L. infantum. As for the immunocompetent patients with untreated active VL its impact is limited, whilst immunosupressed patients are the most infectious towards sand flies. Thus, the screening for latent Leishmania infection in HIV-infected patients is recommended in scenarios where transmission occurs.

Can the dexamethasone intravitreal implant Ozurdex be safely administered in an out-of-operating room setting?

Purpose

To describe a standardized protocol of the dexamethasone intravitreal (DEX) implant Ozurdex (Allergan, Dublin, Ireland) performed in a controlled environment surgical cabin (CESC).

Methods

Retrospective and observational study conducted on patients who underwent a DEX implant between May 2011 and June 2019, in a third level University Hospital. The controlled environment surgical cabin (ArcSterile, Imex, Valencia, Spain) used in this study was the MB 20 (2 m width, 1.60 m depth, and 2 m height) with an uninterrupted power system (ARSSAI1) to keep the cabin working for 20 min. The cabin was used in the open mode. A standardized protocol of intravitreal injections in controlled environment surgical cabin was designed.

Results

From May 2011 to February 2015, a total of 454 DEX implants were performed in the operating room, whereas from March 2015 to June 2019, 1054 DEX devices were implanted using the CESC. The mean number of DEX implants/per week was significantly lower in the operating room than in the CESC [2.3 (2.1 to 2.5) versus 3.8 (3.6 to 4.1), mean difference 1.5 (1.2 to 1.8), p < 0.0001]. The incidence of endophthalmitis was similar in the two populations, 0/454 (0.0%; 95% CI 0.0 to 0.81%) and 0/1054 (0.0%; 95% CI 0.0 to 0.35%) in the operating room and in the CESC, respectively.

Conclusions

The CESC may be a good alternative to the conventional operating room for the administration of the intravitreal DEX implant.

Spanish validation of the self-evaluation of negative symptoms scale SNS in an adolescent population

BACKGROUND

Negative symptoms (NS) may be observed in the general population in an attenuated form and in high-risk mental states. However, they have been less studied in the general population than positive symptoms, in spite of their importance at the insidious onset of schizophrenia and their appearance before positive symptoms. This study aimed to analyze the empirical structure of the Spanish version of the Self-Evaluation of Negative Symptoms (SNS) Scale and find its psychometric properties and invariance of measurement across sex and age in a sample of adolescents.

METHODS

The sample consisted of 4521 adolescents (53.6% female) from 11 to 18 years of age.

RESULTS

Confirmatory Factor Analysis of the SNS confirmed an internal structure of five first-order factors by the characteristic dimensions of NS: avolition, social withdrawal, diminished emotional range, anhedonia, alogia, and one second-order factor which includes the total NS score. Multi-group confirmatory factor analysis showed that the scale was invariant across sex and age. Total scale reliability was adequate. A strong relationship was found between the SNS with depressive symptomatology, moderate with ideas of reference and low with aberrant salience.

CONCLUSION

The results back use of the Spanish version of the SNS scale for detection of NS in the general population of adolescents.

Surfactant-templated zeolites for the production of active pharmaceutical intermediates

A hierarchical USY zeolite has been produced using the surfactant-templating method and used as a catalyst for the production of two important active pharmaceutical ingredients. The presence of intracrystalline mesoporosity in the zeolite results in a significant increase in both the activity (up to 30 fold increase in TOF) and reusability for Friedel-Crafts alkylation and aldol condensation steps.

Clinical aspects of visceral leishmaniasis caused by L. infantum in adults. Ten years of experience of the largest outbreak in Europe: what have we learned?

BACKGROUND

An outbreak of leishmaniasis caused by Leishmania infantum was declared in the southwest of the Madrid region (Spain) in June 2009. This provided a unique opportunity to compare the management of visceral leishmaniasis (VL) in immunocompetent adults (IC-VL), patients with HIV (HIV-VL) and patients receiving immunosuppressants (IS-VL).

METHODS

A cohort of adults with VL, all admitted to the Hospital Universitario de Fuenlabrada between June 2009 and June 2018, were monitored in this observational study, recording their personal, epidemiological, analytical, diagnostic, treatment and outcome variables.

RESULTS

The study population was made up of 111 patients with VL (10% HIV-VL, 14% IS-VL, 76% IC-VL). Seventy-one percent of the patients were male; the mean age was 45 years (55 years for the IS-VL patients, P = 0.017). Fifty-four percent of the IC-VL patients were of sub-Saharan origin (P = 0.001). Fever was experienced by 98% of the IC-VL patients vs 73% of the LV-HIV patients (P = 0.003). Plasma ferritin was > 1000 ng/ml in 77% of the IC-VL patients vs 17% of the LV-HIV patients (P = 0.007). Forty-two percent of patients fulfilled the criteria for haemophagocytic lymphohistiocytosis. RDT (rK39-ICT) serological analysis returned sensitivity and specificity values of 45% and 99%, respectively, and ELISA/iIFAT returned 96% and 89%, respectively, with no differences in this respect between patient groups. Fourteen (13.0%) patients with VL experienced treatment failure, eight of whom were in the IC-VL group. Treatment with < 21 mg/kg (total) liposomal amphotericin B (LAB) was associated with treatment failure in the IC-VL patients [P = 0.002 (OR: 14.7; 95% CI: 2.6-83.3)].

CONCLUSIONS

IS-VL was more common than HIV-VL; the lack of experience in dealing with IS-VL is a challenge that needs to be met. The clinical features of the patients in all groups were similar, although the HIV-VL patients experienced less fever and had lower plasma ferritin concentrations. RDT (rK39-ICT) analysis returned a good specificity value but a much poorer sensitivity value than reported in other scenarios. The patients with HIV-VL, IS-VL and IC-VL returned similar serological results. Current guidelines for treatment seem appropriate, but the doses of LAB required to treat patients with HIV-VL and IS-VL are poorly defined.

[Colonization rates by Streptococcus agalactiae in Spanish and foreign pregnant women in the Fuenlabrada University Hospital]

OBJECTIVE

In pregnant women, the rectovaginal colonization by Streptococcus agalactiae (GBS) is related with geographic area of origin (6.5% to 36%). It was analysed GBS carriage in pregnant women in 2012-2014 in our hospital.

METHODS

Observational retrospective study about GBS isolates from rectovaginal samples (RVS) and urine cultures of Spanish and immigrant pregnant women in 2012-2014. It was considered only a single isolation for patient. There were excluded women with GBS in urine samples of RVS study.

RESULTS

A total of 4,648 Spanish and 1,405 immigrant women were analysed. GBS was detected in urine samples in 231 Spanish (5%) and 106 immigrant (7.6%). A total of 5,716 RVS were analysed, GBS was detected in 10.5% of Spanish women and in 18.9% of immigrant women.

CONCLUSIONS

The overall colonization in immigrant women is higher than in Spanish with the exception of Asian women. Cases of GBS detected in urine samples might serve as a possible explanation for the high rate of GBS carriage.

The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation

CRISPR-Cas represents a prokaryotic defense mechanism against invading genetic elements. Although there is a diversity of CRISPR-Cas systems, they all share similar, essential traits. In general, a CRISPR-Cas system consists of one or more groups of DNA repeats named CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), regularly separated by unique sequences referred to as spacers, and a set of functionally associated cas (CRISPR associated) genes typically located next to one of the repeat arrays. The origin of spacers is in many cases unknown but, when ascertained, they usually match foreign genetic molecules. The proteins encoded by some of the cas genes are in charge of the incorporation of new spacers upon entry of a genetic element. Other Cas proteins participate in generating CRISPR-spacer RNAs and perform the task of destroying nucleic acid molecules carrying sequences similar to the spacer. In this way, CRISPR-Cas provides protection against genetic intruders that could substantially affect the cell viability, thus acting as an adaptive immune system. However, this defensive action also hampers the acquisition of potentially beneficial, horizontally transferred genes, undermining evolution. Here we cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle this major dilemma, evolution versus survival.

Evaluation of a Method for Long-Term Cryopreservation of Fungal Strains

The conservation of microorganisms is essential for their in-depth study. However, today's most widely used conservation methods, based on the use of distilled water, soil, oils, or silica, do not guarantee the stability of fungal cells, especially dermatophytes. This problem led us to evaluate the conservation capacity of a cryogenic vials system containing glass beads covered in a cryopreservant hypertonic solution as an alternative method of storage of fungal cells at -80°C. Up to 570 strains of fungi belonging to 27 different species, isolated from clinical samples, were inoculated into cryotubes containing 25 glass beads covered in a cryopreserving hypertonic solution. Suspensions were mixed vigorously and the cryopreserving solution was discarded. The tubes were frozen at -80°C for a period of 42 months and periodically, a glass bead was removed from each cryotube and inoculated onto Sabouraud dextrose agar, and incubated at 30°C for 7-14 days to evaluate the number of colonies recovered, their purity, and phenotypic characteristics. All yeast isolates were recovered, unlike 2 isolates (4.4%) of the mold group and 21 (10.7%) of the dermatophytes. Survival rates were close to 100% for yeasts and molds, with expiration times being estimated for almost indefinite stocks, and 62% for dermatophytes, with an average expiration date of 25.5 years. The phenotypic characteristics remained comparable to those of the strains before storage. Conservation at -80°C using cryogenic vials is a reliable and efficient system for the conservation of fungal collections, and although the behavior differs by groups, stratified survival data are obtained to avoid extinction.

Acceptance, yield and feasibility of attaching HCV birth cohort screening to colorectal cancer screening in Spain

INTRODUCTION

The US Centers for Disease Control recommends hepatitis C virus (HCV) screening for baby boomers. Spain presents a similar distribution of infected patients. We performed a cross sectional prospective study to evaluate the prevalence of undiagnosed HCV infection in subjects born between 1949 and 1974.

METHODS

All out-patients within the age range, both symptomatic and screening procedures, undergoing colonoscopy between December 2014 and June 2015 were offered a HCV antibody blood test and a survey including risk factors for HCV infection and attitude toward HCV screening. Patients with chronic HCV or with a previous negative HCV antibody test were excluded.

RESULTS

A total of 570 subjects, 50% screening procedures, were analyzed. The median age was 55.7, 94.6% were born in Spain and 54.6% were women. Antibodies against HCV were found in 1.6% (95% CI: 0.8-3%) and HCV-RNA in 0.4% (0.1-1.3%). We found no statistically significant differences regarding HCV prevalence, risk factors or socioeconomic characteristics between subjects undergoing colorectal cancer screening and symptomatic subjects.

CONCLUSION

Symptomatic and screening subjects undergoing colonoscopy support HCV screening and present a similar HCV risk profile. Results suggest linking colorectal and HCV screening would yield good results.

Interleukin-2 as a marker for detecting asymptomatic individuals in areas where Leishmania infantum is endemic

No field method exists for identifying asymptomatic individuals in areas where Leishmania infantum is endemic. This work reports that, 24 h after stimulating whole blood with soluble Leishmania antigen (SLA), plasma interferon-γ (IFN-γ) and interleukin-2 (IL-2) become significantly elevated in samples from asymptomatic individuals (n=47) compared with those from negative controls (n=50), all of them recruited from a blood bank. When compared with the reference test SLA-lymphoproliferative assay, IL-2 appears as a new, 100% sensitive and specific marker for asymptomatic individuals with a positive cellular response (compared with 100% and 84.78%, respectively, for IFN-γ). Further studies in other transmission areas and in other cohorts of exposed people need to be performed to confirm these results. Once validated, IFN-γ and IL-2 levels in SLA-stimulated whole blood could be reliably used in the field to estimate the prevalence of those asymptomatic individuals with Leishmania-specific cellular immune responses.

Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast

The RPB1 mutants in the foot region of RNA polymerase II affect the assembly of the complex by altering the correct association of both the Rpb6 and the Rpb4/7 dimer. Assembly defects alter both transcriptional activity as well as the amount of enzyme associated with genes. Here, we show that the global transcriptional analysis of foot mutants reveals the activation of an environmental stress response (ESR), which occurs at a permissive temperature under optimal growth conditions. Our data indicate that the ESR that occurs in foot mutants depends mostly on a global post-transcriptional regulation mechanism which, in turn, depends on Rpb4-mRNA imprinting. Under optimal growth conditions, we propose that Rpb4 serves as a key to globally modulate mRNA stability as well as to coordinate transcription and decay. Overall, our results imply that post-transcriptional regulation plays a major role in controlling the ESR at both the transcription and mRNA decay levels.

CRISPR Content Correlates with the Pathogenic Potential of Escherichia coli

Guide RNA molecules (crRNA) produced from clustered regularly interspaced short palindromic repeat (CRISPR) arrays, altogether with effector proteins (Cas) encoded by cognate cas (CRISPR associated) genes, mount an interference mechanism (CRISPR-Cas) that limits acquisition of foreign DNA in Bacteria and Archaea. The specificity of this action is provided by the repeat intervening spacer carried in the crRNA, which upon hybridization with complementary sequences enables their degradation by a Cas endonuclease. Moreover, CRISPR arrays are dynamic landscapes that may gain new spacers from infecting elements or lose them for example during genome replication. Thus, the spacer content of a strain determines the diversity of sequences that can be targeted by the corresponding CRISPR-Cas system reflecting its functionality. Most Escherichia coli strains possess either type I-E or I-F CRISPR-Cas systems. To evaluate their impact on the pathogenicity of the species, we inferred the pathotype and pathogenic potential of 126 strains of this and other closely related species and analyzed their repeat content. Our results revealed a negative correlation between the number of I-E CRISPR units in this system and the presence of pathogenicity traits: the median number of repeats was 2.5-fold higher for commensal isolates (with 29.5 units, range 0–53) than for pathogenic ones (12.0, range 0–42). Moreover, the higher the number of virulence factors within a strain, the lower the repeat content. Additionally, pathogenic strains of distinct ecological niches (i.e., intestinal or extraintestinal) differ in repeat counts. Altogether, these findings support an evolutionary connection between CRISPR and pathogenicity in E. coli.

Atypical presentation in adults in the largest community outbreak of leishmaniasis in Europe (Fuenlabrada, Spain)

Since 2009, the largest reported outbreak of leishmaniasis by Leishmania infantum in Europe was reported in Fuenlabrada, Spain. In our hospital, 90 adults with localized leishmanial lymphadenopathy (LLL) or visceral leishmaniasis (VL) were treated during this outbreak; 72% were men, and the mean age was 46.2 years (range 15-95 years). A total of 17 cases (19%) were LLL, an atypical form with isolated lymphadenopathies without other symptoms. All LLL cases occurred in immunocompetent subjects, and only one subject (6%) was a native of sub-Saharan Africa. Diagnosis was performed by fine needle aspiration cytology of the lymphadenopathy. Serology was negative in 38%. LLL outcomes at 6 months were benign, even with doses of liposomal amphotericin B that were often lower (10 mg/kg) than those recommended for VL in Mediterranean areas. A total of 73 subjects (81%) presented with typical VL; 66% of this group were immunocompetent, and 50% of those who were immunocompetent were descendants of natives of sub-Saharan Africa. The rK39 test and polymerase chain reaction were the most useful tests for confirmation of the diagnosis. An initial response to treatment was observed in 99% of cases, and relapses occurred in 14% of cases. Leishmaniasis should be included in the differential diagnosis of isolated lymphadenopathies in endemic areas. LLL could be considered a more benign entity, one different than VL, and less aggressive management should be studied in future investigations.

CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli

Prokaryotes immunize themselves against transmissible genetic elements by the integration (acquisition) in clustered regularly interspaced short palindromic repeats (CRISPR) loci of spacers homologous to invader nucleic acids, defined as protospacers. Following acquisition, mono-spacer CRISPR RNAs (termed crRNAs) guide CRISPR-associated (Cas) proteins to degrade (interference) protospacers flanked by an adjacent motif in extrachomosomal DNA. During acquisition, selection of spacer-precursors adjoining the protospacer motif and proper orientation of the integrated fragment with respect to the leader (sequence leading transcription of the flanking CRISPR array) grant efficient interference by at least some CRISPR-Cas systems. This adaptive stage of the CRISPR action is poorly characterized, mainly due to the lack of appropriate genetic strategies to address its study and, at least in Escherichia coli, the need of Cas overproduction for insertion detection. In this work, we describe the development and application in Escherichia coli strains of an interference-independent assay based on engineered selectable CRISPR-spacer integration reporter plasmids. By using this tool without the constraint of interference or cas overexpression, we confirmed fundamental aspects of this process such as the critical requirement of Cas1 and Cas2 and the identity of the CTT protospacer motif for the E. coli K12 system. In addition, we defined the CWT motif for a non-K12 CRISPR-Cas variant, and obtained data supporting the implication of the leader in spacer orientation, the preferred acquisition from plasmids harboring cas genes and the occurrence of a sequential cleavage at the insertion site by a ruler mechanism.

Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (cas) genes conform the CRISPR-Cas systems of various bacteria and archaea and produce degradation of invading nucleic acids containing sequences (protospacers) that are complementary to repeat intervening spacers. It has been demonstrated that the base sequence identity of a protospacer with the cognate spacer and the presence of a protospacer adjacent motif (PAM) influence CRISPR-mediated interference efficiency. By using an original transformation assay with plasmids targeted by a resident spacer here we show that natural CRISPR-mediated immunity against invading DNA occurs in wild type Escherichia coli. Unexpectedly, the strongest activity is observed with protospacer adjoining nucleotides (interference motifs) that differ from the PAM both in sequence and location. Hence, our results document for the first time native CRISPR activity in E. coli and demonstrate that positions next to the PAM in invading DNA influence their recognition and degradation by these prokaryotic immune systems.

Diversity of CRISPR loci in Escherichia coli

CRISPR (clustered regularly interspaced short palindromic repeats) and CAS (CRISPR-associated sequence) proteins are constituents of a novel genetic barrier that limits horizontal gene transfer in prokaryotes by means of an uncharacterized mechanism. The fundamental discovery of small RNAs as the guides of the defence apparatus arose as a result of Escherichia coli studies. However, a survey of the system diversity in this species in order to further contribute to the understanding of the CRISPR mode of action has not yet been performed. Here we describe two CRISPR/CAS systems found in E. coli, following the analysis of 100 strains representative of the species' diversity. Our results substantiate different levels of activity between loci of both CRISPR types, as well as different target preferences and CRISPR relevances for particular groups of strains. Interestingly, the data suggest that the degeneration of one CRISPR/CAS system in E. coli ancestors could have been brought about by self-interference.

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated CRISPR-associated sequence (CAS) proteins constitute a novel antiviral defence system that is widespread in prokaryotes. Repeats are separated by spacers, some of them homologous to sequences in mobile genetic elements. Although the whole process involved remains uncharacterized, it is known that new spacers are incorporated into CRISPR loci of the host during a phage challenge, conferring specific resistance against the virus. Moreover, it has been demonstrated that such interference is based on small RNAs carrying a spacer. These RNAs would guide the defence apparatus to foreign molecules carrying sequences that match the spacers. Despite this essential role, the spacer uptake mechanism has not been addressed. A first step forward came from the detection of motifs associated with spacer precursors (proto-spacers) of Streptococcus thermophilus, revealing a specific recognition of donor sequences in this species. Here we show that the conservation of proto-spacer adjacent motifs (PAMs) is a common theme for the most diverse CRISPR systems. The PAM sequence depends on the CRISPR-CAS variant, implying that there is a CRISPR-type-specific (motif-directed) choice of the spacers, which subsequently determines the interference target. PAMs also direct the orientation of spacers in the repeat arrays. Remarkably, observations based on such polarity argue against a recognition of the spacer precursors on transcript RNA molecules as a general rule.

Rhinocerebral zygomycosis caused by Saksenae vasiformis in a diabetic patient

We report a rare case of invasive rhinocerebral Saksenae vasiformis infection in a 71-year-old man with type 2 diabetes mellitus ketoacidosis. Combined histological and microbiological examination of two biopsy specimens taken at four days' intervals showed broad non-septate hyphae on direct smears of biopsies and necrosis and angioinvasion by hyphae were seen in the tissue. S. vasiformis was cultured from both biopsies. The patient had a fatal outcome even though partial debridement, liposomal amphotericin B treatment and control of diabetes were instituted. Permission for necropsy was denied. Clinical, epidemiological and pathological features of the case and manifestations of S. vasiformis infections are discussed. Most cases involve cutaneous sites and only two cases of rhinocerebral infections (both with fatal outcome) have been described. The present case is the third documented case of involvement of the sinuses and the second case of S. vasiformis infection documented in Europe.

Viral monitoring and successful treatment of a ganciclovir-resistant cytomegalovirus infection in a heart transplant recipient

We reported a ganciclovir (GCV)-resistant cytomegalovirus (CMV) infection in a heart transplant recipient. Genotypic and phenotypic susceptibility assays demonstrated an A594V mutation in the UL97 phosphotransferase gene and GCV IC(50)>96 microM. Low GCV concentration exposure, immunosuppressive treatment, donor-positive/recipient-negative CMV serostatus, viral reactivations within antiviral prophylaxis or treatment, contributed to GCV-resistant strain selection.

Saccharomyces cerevisiae signature genes for predicting nitrogen deficiency during alcoholic fermentation

Genome-wide analysis of the wine yeast strain Saccharomyces cerevisiae PYCC4072 identified 36 genes highly expressed under conditions of low or absent nitrogen in comparison with a nitrogen-replete condition. Reverse transcription-PCR analysis for four of these transcripts with this strain and its validation with another wine yeast strain underlines the usefulness of these signature genes for predicting nitrogen deficiency and therefore the diagnosis of wine stuck/sluggish fermentations.

Evolution of the antimicrobial resistance of Pseudomonas aeruginosa in Spain: second national study (2003)

The second national prevalence study of Pseudomonas aeruginosa has been carried out in Spain. A total of 1250 clinical isolates of P. aeruginosa were collected from 127 hospitals in 1 week in 2003 and the resistance data gathered from the isolates was compared with those of the first study in 1998 (1014 isolates from 136 hospitals). Antimicrobial susceptibility testing was performed in both studies in the same laboratory. The most active antimicrobials were piperacillin, piperacillin-tazobactam, and amikacin (< or =10% resistant) and resistance to these antimicrobials did not change over the time. The least active were ofloxacin and gentamicin (> or =30% resistant). From 1998 to 2003, resistance increased significantly to ciprofloxacin (23% vs. 28%, respectively, p=0.015); ofloxacin (30% vs. 37%, p=0.002); imipenem (14% vs. 18%, p=0.017) and meropenem (8% vs. 13%, p <0.001). Resistance to aztreonam (23%), ceftazidime (16%), cefepime (20%), ticarcillin (13%) and tobramycin (11%) remained stable. Isolates from inpatients were significantly more resistant than those from outpatients to all antimicrobials, with the exception of fluoroquinolones and aminoglycosides (p <0.01). Isolates from outpatients were significantly more resistant to these two groups (p <0.05) than to other antimicrobials. In Spain, from 1998 to 2003, the susceptibility pattern of P. aeruginosa to antimicrobial agents has changed. Isolates have become significantly more resistant to fluoroquinolones and carbapenems. However, resistance to beta-lactams and aminoglycosides remains stable.

Ultrasonic tissue characterization for monitoring nanostructured TiO2-induced bone growth

The use of bioactive nanostructured TiO2 has recently been proposed for improving orthopaedic implant adhesion due to its improved biocompatibility with bone, since it induces: (i) osteoblast function, (ii) apatite nucleation and (iii) protein adsorption. The present work focuses on a non-ionizing radiation emitting technique for quantifying in real time the improvement in terms of mechanical properties of the surrounding bone due to the presence of the nanostructured TiO2 prepared by controlled precipitation and acid ageing. The mechanical strength is the ultimate goal of a bone implant and is directly related to the elastic moduli. Ultrasonics are high frequency mechanical waves and are therefore suited for characterizing elastic moduli. As opposed to echographic techniques, which are not correlated to elastic properties and are not able to penetrate bone, a low frequency ultrasonic transmission test is proposed, in which a P-wave is transmitted through the specimen and recorded. The problem is posed as an inverse problem, in which the unknown is a set of parameters that describe the mechanical constants of the sequence of layers. A finite element numerical model that depends on these parameters is used to predict the transformation of the waveform and compare to the measurement. The parameters that best describe the real tissue are obtained by minimizing the discrepancy between the real and numerically predicted waveforms. A sensitivity study to the uncertainties of the model is performed for establishing the feasibility of using this technique to investigate the macroscopic effect on bone growth of nanostructured TiO2 and its beneficial effect on implant adhesion.

Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation

Gene expression profiles of a wine strain of Saccharomyces cerevisiae PYCC4072 were monitored during alcoholic fermentations with three different nitrogen supplies: (i) control fermentation (with enough nitrogen to complete sugar fermentation), (ii) nitrogen-limiting fermentation, and (iii) the addition of nitrogen to the nitrogen-limiting fermentation (refed fermentation). Approximately 70% of the yeast transcriptome was altered in at least one of the fermentation stages studied, revealing the continuous adjustment of yeast cells to stressful conditions. Nitrogen concentration had a decisive effect on gene expression during fermentation. The largest changes in transcription profiles were observed when the early time points of the N-limiting and control fermentations were compared. Despite the high levels of glucose present in the media, the early responses of yeast cells to low nitrogen were characterized by the induction of genes involved in oxidative glucose metabolism, including a significant number of mitochondrial associated genes resembling the yeast cell response to glucose starvation. As the N-limiting fermentation progressed, a general downregulation of genes associated with catabolism was observed. Surprisingly, genes encoding ribosomal proteins and involved in ribosome biogenesis showed a slight increase during N starvation; besides, genes that comprise the RiBi regulon behaved distinctively under the different experimental conditions. Here, for the first time, the global response of nitrogen-depleted cells to nitrogen addition under enological conditions is described. An important gene expression reprogramming occurred after nitrogen addition; this reprogramming affected genes involved in glycolysis, thiamine metabolism, and energy pathways, which enabled the yeast strain to overcome the previous nitrogen starvation stress and restart alcoholic fermentation.

PCR en tiempo real, inmunofluorescencia y cultivo para la detección de Bordetella pertussis: evaluación prospectiva y epidemiología molecular

INTRODUCTION

An increase in the incidence of pertussis has been observed in recent years. The aim of this study was to determine the usefulness of several procedures, including real-time PCR, for the laboratory diagnosis of pertussis, and to investigate clonal relationships among clinical isolates of Bordetella pertussis.

METHODS

During the period of August 2002 to October 2003, nasopharyngeal swabs were collected from pediatric and adult patients with symptoms of pertussis, and contact cases. The samples were processed by culture, direct fluorescence assay (DFA), and real-time PCR. Most of the isolates were further characterized by pulsed-field gel electrophoresis (PFGE).

RESULTS

Among 121 clinical samples corresponding to 117 patients, B. pertussis was detected in 17 samples by culture (14.1%), 30 samples (24.8%) by DFA and 41 samples (33.9%) by real-time PCR. Real-time PCR diagnosed 26 and 24 more cases than culture and DFA, respectively. Seventeen clinical isolates were available for PFGE analysis, 14 collected during the study period and three in 1997, 2000 and 2001. PFGE identified 5 different genotypes, 2 of which included 8 (genotype C) and 6 (genotype E) isolates. Two of the older isolates (1997 and 2001) were identified as genotype C.

CONCLUSION

Real-time PCR applied to the diagnosis of pertussis provided more positive results than DFA and culture, but the true diagnostic value of these results should be clarified. Two bacterial clones were dominant, and one of them has circulated at least since 1997.

Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements

Prokaryotes contain short DN repeats known as CRISPR, recognizable by the regular spacing existing between the recurring units. They represent the most widely distributed family of repeats among prokaryotic genomes suggesting a biological function. The origin of the intervening sequences, at present unknown, could provide clues about their biological activities. Here we show that CRISPR spacers derive from preexisting sequences, either chromosomal or within transmissible genetic elements such as bacteriophages and conjugative plasmids. Remarkably, these extrachromosomal elements fail to infect the specific spacer-carrier strain, implying a relationship between CRISPR and immunity against targeted DNA. Bacteriophages and conjugative plasmids are involved in prokaryotic population control, evolution, and pathogenicity. All these biological traits could be influenced by the presence of specific spacers. CRISPR loci can be visualized as mosaics of a repeated unit, separated by sequences at some time present elsewhere in the cell.

CYGD: the Comprehensive Yeast Genome Database

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.

Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 1 21 78T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax

Two strains of a novel bacterium were isolated independently of each other, from different depths in the Mediterranean Sea, within a time period of 7 months, using two different isolation approaches that were focused on different objectives. Both strains, designated ISO1 and ISO4T, were halophilic, Gram-negative, strictly aerobic, straight rods that were oxidase- and catalase-positive. Both strains produced mucoid colonies in some defined minimal media and were able to grow with organic acids and some alkanes; they were also able to accumulate intracellular poly-beta-hydroxybutyrate granules. The G + C content of the DNA of strain ISO4T was 66 mol%. Comparative analysis of 16S rRNA gene sequences showed that the closest described species to the novel strains were Alcanivorax borkumensis and Fundibacter jadensis, both of the gamma-Proteobacteria. Both of these recognized species were originally isolated from North Sea waters and are able to degrade aliphatic compounds, a property shared with strains ISO1 and ISO4T. However, strains ISO1 and ISO4T were different from A. borkumensis and F. jadensis, not only in their 16S rDNA sequences but also in the motility of their cells (by polar flagella) and by the presence of C19:Ocyclo in their cellular fatty acids, among other differential features. On the basis of biochemical and molecular data, it is suggested that strains ISO1 and ISO4T be recognized as a novel species of the genus Alcanivorax, for which the name Alcanivorax venustensis (ISO4T =DSM 13974T =CECT 5388T) is proposed. On the basis of its high phenotypic similarity and close phylogenetic relatedness to A. borkumensis, it is also proposed that F. jadensis (DSM 12178T) be reclassified as Alcanivorax jadensis in the genus Alcanivorax, and that the description of the genus Alcanivorax be emended.

Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions

The presence, prevalence and variability of microorganisms related to the species Alteromonas macleodii, a well known culturable gamma-Proteobacterium, has been studied in different seawater samples from diverse geographical locations, in both the Northern and Southern hemispheres, and tested with two molecular techniques (rRNA hybridization and gene cloning and sequencing). Results show that A. macleodii-like microorganisms are present in high proportions in North Atlantic and, especially, Mediterranean waters, being higher at deep samples and particle-associated fractions, in agreement with previous findings. In contrast, Southern samples (all from very cold areas near Antarctica) presented no significant hybridization signals. The analysis of the ribosomal ITS (16S-23S internal transcribed spacers) revealed that A. macleodii-like microorganisms from Mediterranean, North Atlantic, Caribbean and Red Sea waters differed in both size and sequence, mostly depending on their geographical origin, with Mediterranean and North Atlantic clones clustering into two main groups whereas Caribbean and Red Sea clones appeared separated.

Molecular characterization of a Spanish isolate of Mycobacterium malmoense

We present the genomic characterization of a Spanish isolate of Mycobacterium malmoense. Identification and molecular characterization of the microorganism were performed using the technique of PCR-restriction fragment length polymorphism analysis (PRA) and sequencing of the 16S and the ITS spacer (16S-23S rDNA intergenic spacer region). It was seen that our isolate is very similar to the strain described in Sweden, but differs in the sequencing of the ITS from the isolate in Great Britain. Molecular techniques facilitate a rapid diagnosis and enable a better understanding of the epidemiology of this microorganism.

Application of molecular biology techniques to the diagnosis of nontuberculous mycobacterial infections

A total of 19,723 clinical samples were cultivated for the detection of mycobacteria from January 1995 to March 2001. The 203 strains of nontuberculous mycobacteria isolated were identified with the use of molecular techniques in combination with traditional biochemical tests. The molecular methods applied were PCR-restriction fragment length polymorphism analysis (PRA) alone or in combination with 16S rRNA and 16S-23S spacer sequencing. The patient records of those with specimens positive for mycobacteria were analysed to evaluate the clinical significance of the culture results. Twenty-five of the 124 patients analysed (20%) were regarded as having clinical mycobacteriosis. The main species associated with mycobacteriosis were: Mycobacterium avium (13 cases), M. intracellulare (2 cases), M. kansasii (5 cases), M. chelonae (2 cases), M. malmoense (1 case), M. scrofulaceum (1 case) and M. marinum (1 case). The use of PRA alone or in combination with gene sequencing provided valuable help in discerning mycobacteria at both the intra- and interspecies level, thus contributing to a faster and more efficient diagnosis and epidemiological follow-up.

RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions

A novel database, under the acronym RISSC (Ribosomal Intergenic Spacer Sequence Collection), has been created. It compiles more than 1600 entries of edited DNA sequence data from the 16S-23S ribosomal spacers present in most prokaryotes and organelles (e.g. mitochondria and chloroplasts) and is accessible through the Internet (http://ulises.umh.es/RISSC), where systematic searches for specific words can be conducted, as well as BLAST-type sequence searches. Additionally, a characteristic feature of this region, the presence/absence and nature of tRNA genes within the spacer, is included in all the entries, even when not previously indicated in the original database. All these combined features could provide a useful documentation tool for studies on evolution, identification, typing and strain characterization, among others.

Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I

The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S-23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro-organisms. In terms of community structure, our results show that although depth-related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface-associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well-defined taxonomic units.

Genetic differentiation in the striped dolphin Stenella coeruleoalba from European waters according to mitochondrial DNA (mtDNA) restriction analysis

We used mitochondrial DNA (mtDNA) restriction analysis to study genetic variation in 98 striped dolphins (Stenella coeruleoalba) stranded on coasts from different European countries and from animals caught by fisheries. A total of 63 different restriction sites was mapped after digestion of mtDNA with 15 restriction endonucleases that yielded a total of 27 haplotypes. No haplotype was shared between Mediterranean and Atlantic areas. All the analyses indicate the existence of two different populations with a very limited gene flow across the Strait of Gibraltar.

Use of the 16S--23S ribosomal genes spacer region in studies of prokaryotic diversity

The description of microbial diversity by molecular culture-independent techniques most often involves the amplification of the 16S rRNA by PCR gene and either analysis of the diversity of amplified molecules (community fingerprinting) that allows the simultaneous study of many samples or the cloning and sequencing of a significant amount of amplification products. The fact that between the 16S and the 23S genes in the ribosomal operon there is a spacer extremely variable in both sequence and length provides an excellent tool to simplify both approaches. The spacer can be amplified almost as easily as the 16S rDNA taking advantage of conserved nucleotide stretches at the 5' end of the 23S gene and the amplicon can contain different amounts of the 16S rDNA choosing primers at the different conserved areas within this gene. Identified by the acronym RISA (rDNA internal spacer analysis), the spacer addition provides a marker of highly variable size allowing standard separation of the amplification products and the sequence of this hypervariable region is useful in the fine discrimination of operational taxonomic units.